RR and EDA report fixes and improvements. 1) Got closer to generating working references to report's figures. <TODO>: a) figure out why knitr now includes figures, using .Rmd style (![]) instead of LaTeX (\includegraphics{}); b) consider using hook function (see "sandbox/knitr-rmd")</TODO>. 2) Added hook function example for LaTeX. 3) Updated Makefile (for .Rnw: 'pdflatex' - second pass to resolve references) and code cleanup.